User: keegan

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keegan60
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keegankorthauer
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2 years, 10 months ago
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Posts by keegan

<prev • 18 results • page 1 of 2 • next >
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Comment: C: unequal sample sizes in groups for testCovariate argument in dmrseq
... Hi Stephanie, Thanks for your questions. (1) First, the unequal sample sizes per group are not a problem; `dmrseq` does not assume equal sample sizes in each level. You will need to filter out any sites that are not covered in at least two samples per group however. (2) Yes, you are correct. You ...
written 9 weeks ago by keegan60
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Answer: A: Using surrogate variables as covariates in WGBS differential methylation calling
... Hi, Great question. I'm not aware of any publications that perform SVA on WGBS data to adjust for batch effects. However, in principle, you could do so following the same principles of microarray, RNAseq, etc data. While SVA may have originally been developed for normally distributed data, I am not ...
written 3 months ago by keegan60
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Answer: A: dmrseq error: promise already under evaluation??
... Hi, Thank you for sending the example object. I was able to track down the issue and just pushed a fix (the bug was introduced by a recent commit). Using the latest version, I am able to run dmrseq successfully on the object. The latest versions are available on Github immediately and through Bioc ...
written 3 months ago by keegan60
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Comment: C: dmrseq error: promise already under evaluation??
... Thanks for checking on the version and dependencies. If a single chromosome runs fine, this might be an out of memory issue. If the file is too large, shoot me an email and I'll send you back a link where you can upload it. Best, Keegan ...
written 3 months ago by keegan60
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Comment: C: dmrseq error: promise already under evaluation??
... Hi, Thank you for reporting this issue. Can you verify which version of dmrseq you are using, and check that all other packages are up to date (using BiocManager::valid())? If you are using a current version with updated dependencies and the error still persists, would you be able to send along a ...
written 3 months ago by keegan60
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Comment: C: dmrseq installation failed
... Looks like this issue has now been resolved and bumphunter is passing build in Bioconductor 3.8. ...
written 11 months ago by keegan60
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Answer: A: Internal bug of DMR-Seq?
... Hi Deepak, Thanks for sending the files. I was able to track down the issue and make a fix. The problem was related to improper handling of very small chromosomes that end up with zero coverage after filtering loci. After applying the fix, the latest version of dmrseq runs your code without errors ...
written 11 months ago by keegan60
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Comment: C: Internal bug of DMR-Seq?
... Thanks for checking on that. I'm not sure where this error is coming from. Would it be possible to send me a small test .rds file that contains the BSseq input object - could just contain the offending chromosome GL4563591 - along with the code used to call dmrseq? If I can reproduce the problem, it ...
written 11 months ago by keegan60
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Comment: C: Internal bug of DMR-Seq?
... Can you inspect the output of BiocManager::valid() ? If it indicates that any packages are out of date, please try updating them and trying again. ...
written 11 months ago by keegan60
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Answer: A: Internal bug of DMR-Seq?
... I think I found the most likely cause of the error being thrown. Essentially, I don't think the error handling for region-level model fitting was correct when the covariate of interest is a multi-level factor. When a region fit failed to converge, it would output a row to the results table that assu ...
written 12 months ago by keegan60

Latest awards to keegan

Scholar 11 months ago, created an answer that has been accepted. For A: dmrseq: cannot adjust for a covariate
Scholar 14 months ago, created an answer that has been accepted. For A: dmrseq: cannot adjust for a covariate
Scholar 2.6 years ago, created an answer that has been accepted. For A: dmrseq: cannot adjust for a covariate

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